This section shows some graphics about the processed data. The data consists in three .csv files:
metadata.csv
hplc.csv
absorption.csv
sample_id 438116 was duplicated and removed from the data.
Will be using depth instead of pressure to characterize the depth of the measurements.
Will be only using observations measured in the first 2 meters of the water column. All the following graphs will be using data measured between 0-2 meters.
Now, this table shows the metadata that have no HPLC values associated.
These are the absorption spectra with no HPLC association.
Most of the data is from the Scotian Shelf, Labrador Sea and Scotian Shelf and Slope.
The number of observation is also relatively stable through the years.
Observations were classified into bioregions based on the following criteria (where position is south if latitude < 48):
bathymetry > -300 & position == "North" ~ "Labrador & Greenland Shelves (LGS)"
bathymetry <= -300 & position == "North" ~ "Labrador Sea Basin (LSB)"
bathymetry >= -300 & position == "South" & yday <= 180 ~ "Scotian Shelf Spring (SSSp)"
bathymetry >= -300 & position == "South" & yday > 180 ~ "Scotian Shelf Fall (SSFa)"
bathymetry < -300 & position == "South"~ "Northwest Atlantic Basin ocean (NAB)"0 in the HPLC data. After discussions, they are true 0 and not missing values.Some HPLC sample_id were not numeric (ex.: FL002), I removed them from the data.
There are hplchla and hplcchla variables in the data. I have merge both columns into one because I suspect it is an error and should be the same variable.
but19 was summed as but19 + butlike.
hex19 was summed as hex19 + hexlike + hexlike2.
I have calculated aphy_specific using hplcchla.
Here is an attempt to visualize the seasonal cycle of few pigments. I have calculated the average pigment concentration and then the average total concentration to finally calculate the relative average contribution of each pigment.
Here is how I named absorption data:
anap is the data contained in files with detritus in their name.ap is the data contained in files with particulate in their name.aphy is the data contained in files with phytoplankton in their name.Absorption spectra with any values <= 0 between 350 and 400 nm have been removed.
Absorption spectra with aphy(440) < aphy(410) have been removed (possible problem with pigment extraction).
We can observe that there is a specific absorption gradient among bioregions.
The fit was done for data between 380 and 730 nm, excluding the 400–480 and 620–710 nm ranges to avoid any residual pigment absorption that might still have been present after sodium hypochlorite treatment (Babin 2003).
A R2 of 0.90 was used to filter out bad models.
Labrador & Greenland Shelves (LGS), there are only data in May/June. It is not enough to get insights on the seasonal cycles. At the moment, I am not sure how to deal with that.Northwest Atlantic Basin ocean (NAB) we can clearly see the seasonal pattern of hex19.Explore and try to understand the method of Emmanuel that aims to decompose absorption spectra into two populations.
In this section, I put our data in the context of the paper by Bricaud et al. (1995).
\[ a^*_\phi(\lambda) = A(\lambda)\times\text{chl-a}^{-B(\lambda)} \]
Based on the linear relationships in the previous graph, this shows the R2 as a function of the wavelength.
In this section we explore how the Apparent visible wavelength (AVW) could be used to describe the spectral shape of phytoplankton absorption. The AVW index is calculated following (Vandermeulen et al. 2020).
This graph shows all the phytoplankton absorption spectra colored by the value of the calculated AVW.
Attention: These numbers are based on the total number of reported stations. For example, in 2019, there are a total of 217 stations, but only 71 of them have absorption measurements.
There are some unusual bumps around 530 nm. We should have a closer look at the raw data.
Within each panel, we can see the averaged spectra and a subset of 100 randomly selected spectra by bioregion and type of absorption.
The observed nonlinearity between Chl_a and the ratio of phytoplankton absorption aph (443)/aph (670) indicating the packaging effect and changes in the intercellular composition of pigments.
Numbers at the right represent: mean (min - max).
This aphy* ratio was found to correlate with phytoplankton cell size. That is cool to see that PAAW correlates with it! Using PAAW to infer aphy* means that we do not have to measure chla (HPLC or other ways).